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kiyoonkiyoon
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refactor!: much better typing and API
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‎pyproject.toml

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[tool.pytest.ini_options]
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addopts = "--cov=ml_project" # CHANGE (name of the importing module name)
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testpaths = ["tests"]
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[tool.ruff]
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src = ["src"] # for ruff isort
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namespace-packages = ["tools", "scripts"] # for INP rule, suppress on these directories
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[tool.ruff.lint]
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# OPTIONALLY ADD MORE LATER
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select = [
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# flake8
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"E",
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"F",
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"W",
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"B", # Bugbear
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"D", # Docstring
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"D213", # Multi-line docstring summary should start at the second line (replace D212)
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"N", # Naming
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"C4", # flake8-comprehensions
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"UP", # pyupgrade
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"SIM", # simplify
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"RUF", # ruff-specific
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"RET501", # return
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"RET502", # return
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"RET503", # return
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"PTH", # path
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"NPY", # numpy
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"PD", # pandas
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"PYI", # type stubs for pyright/pylance
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"PT", # pytest
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"PIE", #
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"LOG", # logging
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"COM818", # comma misplaced
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"COM819", # comma
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"DTZ", # datetime
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"YTT",
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"ASYNC",
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"FBT", # boolean trap
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"A", # Shadowing python builtins
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"EXE", # executable (shebang)
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"FA", # future annotations
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"ISC", # Implicit string concatenation
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"ICN", # Import convention
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"INP", # Implicit namespace package (no __init__.py)
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"Q", # Quotes
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"RSE", # raise
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"SLOT", # __slots__
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"PL", # Pylint
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"TRY", # try
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"FAST", # FastAPI
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"AIR", # airflow
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"DOC", # docstring
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# Not important
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"T10", # debug statements
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"T20", # print statements
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]
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ignore = [
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"E402", # Module level import not at top of file
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"W293", # Blank line contains whitespace
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"W291", # Trailing whitespace
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"D10", # Missing docstring in public module / function / etc.
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"D200", # One-line docstring should fit on one line with quotes
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"D212", # Multi-line docstring summary should start at the first line
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"D417", # require documentation for every function parameter.
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"D401", # require an imperative mood for all docstrings.
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"DOC201", # missing Return field in docstring
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"PTH123", # Path.open should be used instead of built-in open
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"PT006", # Pytest parameterize style
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"N812", # Lowercase `functional` imported as non-lowercase `F` (import torch.nn.functional as F)
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"NPY002", # legacy numpy random
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"UP017", # datetime.timezone.utc -> datetime.UTC
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"SIM108", # use ternary operator instead of if-else
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"TRY003", # long message in except
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]
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[tool.ruff.lint.pydocstyle]
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convention = "google"
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[tool.ruff.lint.pycodestyle]
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# Black or ruff will enforce line length to be 88, except for docstrings and comments.
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# We set it to 120 so we have more space for docstrings and comments.
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max-line-length = 120
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[tool.ruff.lint.isort]
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# combine-as-imports = true
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known-third-party = ["wandb"]
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## Uncomment this if you want to use Python < 3.10
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# required-imports = [
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# "from __future__ import annotations",
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# ]
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[tool.ruff.lint.flake8-tidy-imports]
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# Ban certain modules from being imported at module level, instead requiring
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# that they're imported lazily (e.g., within a function definition, if TYPE_CHECKING, etc.)
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# NOTE: Ruff code TID is currently disabled, so this settings doesn't do anything.
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banned-module-level-imports = ["torch", "tensorflow"]
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[tool.ruff.lint.pylint]
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max-args = 10
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max-bool-expr = 10
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max-statements = 100
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[tool.pyright]
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include = ["src"]
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typeCheckingMode = "standard"
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useLibraryCodeForTypes = true
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autoImportCompletions = true
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# pythonPlatform = "Linux"

‎python/pyproject.toml

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Original file line numberDiff line numberDiff line change
@@ -31,118 +31,3 @@ keywords = ["biology"]
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[tool.setuptools.packages.find]
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where = ["src"]
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[tool.pytest.ini_options]
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addopts = "--cov=ml_project" # CHANGE (name of the importing module name)
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testpaths = ["tests"]
38-
39-
[tool.ruff]
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src = ["src"] # for ruff isort
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namespace-packages = ["tools", "scripts"] # for INP rule, suppress on these directories
42-
43-
[tool.ruff.lint]
44-
# OPTIONALLY ADD MORE LATER
45-
select = [
46-
# flake8
47-
"E",
48-
"F",
49-
"W",
50-
"B", # Bugbear
51-
"D", # Docstring
52-
"D213", # Multi-line docstring summary should start at the second line (replace D212)
53-
"N", # Naming
54-
"C4", # flake8-comprehensions
55-
"UP", # pyupgrade
56-
"SIM", # simplify
57-
"RUF", # ruff-specific
58-
"RET501", # return
59-
"RET502", # return
60-
"RET503", # return
61-
"PTH", # path
62-
"NPY", # numpy
63-
"PD", # pandas
64-
"PYI", # type stubs for pyright/pylance
65-
"PT", # pytest
66-
"PIE", #
67-
"LOG", # logging
68-
"COM818", # comma misplaced
69-
"COM819", # comma
70-
"DTZ", # datetime
71-
"YTT",
72-
"ASYNC",
73-
"FBT", # boolean trap
74-
"A", # Shadowing python builtins
75-
"EXE", # executable (shebang)
76-
"FA", # future annotations
77-
"ISC", # Implicit string concatenation
78-
"ICN", # Import convention
79-
"INP", # Implicit namespace package (no __init__.py)
80-
"Q", # Quotes
81-
"RSE", # raise
82-
"SLOT", # __slots__
83-
"PL", # Pylint
84-
"TRY", # try
85-
"FAST", # FastAPI
86-
"AIR", # airflow
87-
"DOC", # docstring
88-
89-
# Not important
90-
"T10", # debug statements
91-
"T20", # print statements
92-
]
93-
94-
ignore = [
95-
"E402", # Module level import not at top of file
96-
"W293", # Blank line contains whitespace
97-
"W291", # Trailing whitespace
98-
"D10", # Missing docstring in public module / function / etc.
99-
"D200", # One-line docstring should fit on one line with quotes
100-
"D212", # Multi-line docstring summary should start at the first line
101-
"D417", # require documentation for every function parameter.
102-
"D401", # require an imperative mood for all docstrings.
103-
"DOC201", # missing Return field in docstring
104-
"PTH123", # Path.open should be used instead of built-in open
105-
"PT006", # Pytest parameterize style
106-
"N812", # Lowercase `functional` imported as non-lowercase `F` (import torch.nn.functional as F)
107-
"NPY002", # legacy numpy random
108-
"UP017", # datetime.timezone.utc -> datetime.UTC
109-
"SIM108", # use ternary operator instead of if-else
110-
"TRY003", # long message in except
111-
]
112-
113-
[tool.ruff.lint.pydocstyle]
114-
convention = "google"
115-
116-
[tool.ruff.lint.pycodestyle]
117-
# Black or ruff will enforce line length to be 88, except for docstrings and comments.
118-
# We set it to 120 so we have more space for docstrings and comments.
119-
max-line-length = 120
120-
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[tool.ruff.lint.isort]
122-
# combine-as-imports = true
123-
known-third-party = ["wandb"]
124-
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## Uncomment this if you want to use Python < 3.10
126-
# required-imports = [
127-
# "from __future__ import annotations",
128-
# ]
129-
130-
[tool.ruff.lint.flake8-tidy-imports]
131-
# Ban certain modules from being imported at module level, instead requiring
132-
# that they're imported lazily (e.g., within a function definition, if TYPE_CHECKING, etc.)
133-
# NOTE: Ruff code TID is currently disabled, so this settings doesn't do anything.
134-
banned-module-level-imports = ["torch", "tensorflow"]
135-
136-
[tool.ruff.lint.pylint]
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max-args = 10
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max-bool-expr = 10
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max-statements = 100
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[tool.pyright]
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include = ["src"]
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typeCheckingMode = "standard"
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useLibraryCodeForTypes = true
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autoImportCompletions = true
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# pythonPlatform = "Linux"

‎python/src/apbs_binary/__init__.py

Lines changed: 75 additions & 47 deletions
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@@ -1,51 +1,79 @@
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import os
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from pathlib import Path
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BIN_DIR = Path(__file__).parent / "bin"
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# NOTE: lib/ only exists for macos arm64, because we built using homebrew
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# and it didn't build entirely statically.
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# Thus we have to pass DYLD_LIBRARY_PATH to the subprocess.run call.
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LIB_DIR = Path(__file__).parent / "lib"
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def bin_path(bin_name: str) -> Path:
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if os.name == "nt":
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return BIN_DIR / f"{bin_name}.exe"
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return BIN_DIR / bin_name
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# bin/
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APBS_BIN_PATH = bin_path("apbs")
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# originally share/apbs/tools/bin/, but moved to bin/
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ANALYSIS_BIN_PATH = bin_path("analysis")
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BENCHMARK_BIN_PATH = bin_path("benchmark")
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BORN_BIN_PATH = bin_path("born")
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COULOMB_BIN_PATH = bin_path("coulomb")
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DEL2DX_BIN_PATH = bin_path("del2dx")
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DX2MOL_BIN_PATH = bin_path("dx2mol")
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DX2UHBD_BIN_PATH = bin_path("dx2uhbd")
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DXMATH_BIN_PATH = bin_path("dxmath")
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MERGEDX_BIN_PATH = bin_path("mergedx")
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MERGEDX2_BIN_PATH = bin_path("mergedx2")
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MGMESH_BIN_PATH = bin_path("mgmesh")
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MULTIVALUE_BIN_PATH = bin_path("multivalue")
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SIMILARITY_BIN_PATH = bin_path("similarity")
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SMOOTH_BIN_PATH = bin_path("smooth")
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TENSOR2DX_BIN_PATH = bin_path("tensor2dx")
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UHBD_ASC2BIN_BIN_PATH = bin_path("uhbd_asc2bin")
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VALUE_BIN_PATH = bin_path("value")
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140
from .executable import (
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ANALYSIS_BIN_PATH,
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APBS_BIN_PATH,
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BENCHMARK_BIN_PATH,
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BIN_DIR,
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BORN_BIN_PATH,
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COULOMB_BIN_PATH,
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DEL2DX_BIN_PATH,
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DX2MOL_BIN_PATH,
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DX2UHBD_BIN_PATH,
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DXMATH_BIN_PATH,
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MERGEDX2_BIN_PATH,
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MERGEDX_BIN_PATH,
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MGMESH_BIN_PATH,
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MULTIVALUE_BIN_PATH,
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SIMILARITY_BIN_PATH,
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SMOOTH_BIN_PATH,
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TENSOR2DX_BIN_PATH,
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UHBD_ASC2BIN_BIN_PATH,
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VALUE_BIN_PATH,
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apbs,
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multivalue,
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process_run,
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popen_analysis,
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popen_apbs,
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popen_benchmark,
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popen_born,
45+
popen_coulomb,
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popen_del2dx,
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popen_dx2mol,
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popen_dx2uhbd,
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popen_dxmath,
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popen_mergedx,
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popen_mergedx2,
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popen_mgmesh,
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popen_multivalue,
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popen_similarity,
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popen_smooth,
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popen_tensor2dx,
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popen_uhbd_asc2bin,
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popen_value,
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run_analysis,
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run_apbs,
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run_benchmark,
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run_born,
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run_coulomb,
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run_del2dx,
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run_dx2mol,
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run_dx2uhbd,
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run_dxmath,
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run_mergedx,
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run_mergedx2,
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run_mgmesh,
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run_multivalue,
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run_similarity,
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run_smooth,
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run_tensor2dx,
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run_uhbd_asc2bin,
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run_value,
2477
)
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__version__ = "0.0.0"
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__all__ = [
29-
"ANALYSIS_BIN_PATH",
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"APBS_BIN_PATH",
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"BENCHMARK_BIN_PATH",
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"BIN_DIR",
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"BORN_BIN_PATH",
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"COULOMB_BIN_PATH",
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"DEL2DX_BIN_PATH",
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"DX2MOL_BIN_PATH",
37-
"DX2UHBD_BIN_PATH",
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"DXMATH_BIN_PATH",
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"MERGEDX2_BIN_PATH",
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"MERGEDX_BIN_PATH",
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"MGMESH_BIN_PATH",
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"MULTIVALUE_BIN_PATH",
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"SIMILARITY_BIN_PATH",
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"SMOOTH_BIN_PATH",
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"TENSOR2DX_BIN_PATH",
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"UHBD_ASC2BIN_BIN_PATH",
47-
"VALUE_BIN_PATH",
48-
"apbs",
49-
"multivalue",
50-
"process_run",
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]

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